def file_manage( public ):
fields = [
db.t_file.f_filename
, db.t_file.f_bionimbus_id
, db.t_file.f_size
, db.t_file.f_reads
]
file_links = [
lambda row: A('Download',_href=URL("default","file_download",args=[row.id]))
]
if is_user_admin( db , auth ):
file_links.append( lambda row: A('Delete',_href=URL("default","file_delete",args=[row.f_filename])) )
if public == True:
q = ( db.t_file.f_bionimbus_id == db.t_experiment_unit.f_bionimbus_id) & ( db.t_experiment_unit.f_is_public == 't' )
else:
if is_user_admin( db , auth ):
q = db.t_file
else:
q = ( db.t_file.f_bionimbus_id == db.t_experiment_unit.f_bionimbus_id) & ( db.t_experiment_unit.f_project == db.t_user_project.f_project_id ) & ( db.t_user_project.f_user_id == auth.user_id )
form = SQLFORM.grid( q ,
fields = fields ,
field_id = db.t_file.id ,
maxtextlength = 200 ,
deletable = False ,
editable = False ,
links = file_links ,
create = False ,
paginate = 1000 ,
selectable = lambda ids: add_file_id(ids) ,
)
return locals()
def project_manage():
if is_user_admin(db, auth):
q = db.t_project.id <> -1
else:
q = (db.t_project.id == db.t_user_project.f_project_id) & (
db.t_user_project.f_user_id == auth.user_id)
return proj(q)
def subproject_manage():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(db.t_subproject.id <> 1,
editable=editable,
create=editable,
deletable=False)
return locals()
def proj(q):
fields = [
db.t_project.id, db.t_project.f_name, db.t_project.f_organism,
db.t_project.f_pi, db.t_project.f_public, db.t_project.f_cloud
]
editable = is_user_admin(db, auth)
links = [
lambda row: A(
'Libraries',
_href=URL(
"default",
'my_experiments?keywords=t_experiment_unit.f_project+=+"%d"' %
(row[db.t_project.id]))),
]
form = SQLFORM.grid(
q,
fields=fields,
#links = project_links ,
editable=editable,
create=editable,
onupdate=auth.archive,
paginate=1000,
links=links,
maxtextlength=150,
deletable=False)
return locals()
def platform_manage():
editable = is_user_admin( db , auth )
form = SQLFORM.grid( db.t_platform ,
create = editable ,
editable = editable ,
deletable = False ,
)
return locals()
def facility_manage():
editable = is_user_admin( db , auth )
form = SQLFORM.grid( db.t_facility ,
create = editable ,
editable = editable ,
deletable = False ,
)
return locals()
def cloud_manage():
editable = is_user_admin( db , auth )
form = SQLFORM.grid( db.t_cloud ,
create = editable ,
editable = editable ,
deletable = editable ,
#fields = fields
)
return locals()
def cloud_manage():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(
db.t_cloud,
create=editable,
editable=editable,
deletable=editable,
#fields = fields
)
return locals()
def sample_states():
editable = is_user_admin( db , auth )
form = SQLFORM.grid( db.t_sample_state ,
create = editable ,
editable = editable ,
deletable = editable ,
paginate = 1000 ,
maxtextlength = 150,
)
return locals()
def platform_manage():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(
db.t_platform,
create=editable,
editable=editable,
deletable=False,
)
return locals()
def facility_manage():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(
db.t_facility,
create=editable,
editable=editable,
deletable=False,
)
return locals()
def file_manage(public):
fields = [
db.t_file.f_filename, db.t_file.f_bionimbus_id, db.t_file.f_size,
db.t_file.f_reads
]
file_links = [
lambda row: A('Download',
_href=URL("default", "file_download", args=[row.id]))
]
if is_user_admin(db, auth):
file_links.append(lambda row: A(
'Delete',
_href=URL("default", "file_delete", args=[row.f_filename])))
if public == True:
q = (db.t_file.f_bionimbus_id == db.t_experiment_unit.f_bionimbus_id
) & (db.t_experiment_unit.f_is_public == 't')
else:
if is_user_admin(db, auth):
q = db.t_file
else:
q = (db.t_file.f_bionimbus_id
== db.t_experiment_unit.f_bionimbus_id) & (
db.t_experiment_unit.f_project
== db.t_user_project.f_project_id) & (
db.t_user_project.f_user_id == auth.user_id)
form = SQLFORM.grid(
q,
fields=fields,
field_id=db.t_file.id,
maxtextlength=200,
deletable=False,
editable=False,
links=file_links,
create=False,
paginate=1000,
selectable=lambda ids: add_file_id(ids),
)
return locals()
def mailing_list_manage():
editable = is_user_admin( db , auth )
form = SQLFORM.grid( db.t_mail_list ,
create = editable ,
editable = editable ,
deletable = editable ,
paginate = 1000 ,
maxtextlength = 150,
#fields = fields
)
return locals()
def sample_states():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(
db.t_sample_state,
create=editable,
editable=editable,
deletable=editable,
paginate=1000,
maxtextlength=150,
)
return locals()
def mailing_list_manage():
editable = is_user_admin(db, auth)
form = SQLFORM.grid(
db.t_mail_list,
create=editable,
editable=editable,
deletable=editable,
paginate=1000,
maxtextlength=150,
#fields = fields
)
return locals()
def user_project_manage():
arg = request.args(0)
fields = [
db.t_user_project.f_project_id, db.t_user_project.f_user_id,
db.t_user_project.f_admin
]
editable = is_user_admin(db, auth)
form = SQLFORM.grid(db.t_user_project,
create=editable,
editable=editable,
deletable=editable,
paginate=1000,
maxtextlength=150,
fields=fields)
#if arg == 'new':
# nfu = names_for_users()
# options = nameval_to_options( nfu )
# form[1][0][1][1] = TD( SELECT( *options , _class="generic-widget" , _id="t_user_project_f_user_id" , _name="f_user_id" ) )
return locals()
def organism_manage():
fields = [
db.t_organism.f_name
, db.t_organism.f_common_name
]
editable = is_user_admin( db , auth )
links = [
lambda row: A( 'Libraries' ,
_href=URL( "default" , 'my_experiments?keywords=t_experiment_unit.f_organism+=+"%d"' % (row[ db.t_organism.id ] ) ) ) ,
]
form = SQLFORM.grid( db.t_organism ,
fields = fields ,
create = editable ,
editable = editable ,
deletable = False ,
onupdate = auth.archive ,
paginate = 1000 ,
maxtextlength = 150 ,
links = links
)
return locals()
def organism_manage():
fields = [db.t_organism.f_name, db.t_organism.f_common_name]
editable = is_user_admin(db, auth)
links = [
lambda row: A(
'Libraries',
_href=URL(
"default",
'my_experiments?keywords=t_experiment_unit.f_organism+=+"%d"' %
(row[db.t_organism.id]))),
]
form = SQLFORM.grid(db.t_organism,
fields=fields,
create=editable,
editable=editable,
deletable=False,
onupdate=auth.archive,
paginate=1000,
maxtextlength=150,
links=links)
return locals()
# ]),
#(T('Sample'),URL('default','sample_manage')==URL(),URL('default','sample_manage'),[]),
#(T('Agent'),URL('default','agent_manage')==URL(),URL('default','agent_manage'),[]),
(T('Key Generation'),URL('keygen','keygen_spreadsheet')==URL(),URL('keygen','keygen_spreadsheet'),[]),
]
u = A('User Documentation',_href='/Bionimbus/static/bd/bd.html',_target='docs')
#u2 = A('Quick start',_href='https://docs.google.com/document/d/1RPb8UEQsDgsZmuDCW_rTEMHtAgGCDnNYTm7BaRsmgAo/view?usp=sharing',_target='docs')
response.menu.append( ( 'Docs' , True , None , [
(T('Documentation'),False,u,[]),
#(T('Quick Start'),False,u2,[])
] ) )
from permissions import is_user_admin
if is_user_admin( db , auth ):
response.menu.append( ( 'Admin' , True , None , [
(T('Sample Tracking'),URL('default','sample_tracking')==URL(),URL('default','sample_tracking'),[]) ,
(T('Project Users'),URL('permissions','user_project_manage')==URL(),URL('permissions','user_project_manage'),[]) ,
(T('Barcodes'),URL('default','barcode_manage')==URL(),URL('default','barcode_manage'),[]) ,
(T('Facilities'),URL('default','facility_manage')==URL(),URL('default','facility_manage'),[]) ,
(T('Mailing Lists'),URL('default','mailing_list_manage')==URL(),URL('default','mailing_list_manage'),[]),
(T('Clouds'),URL('default','cloud_manage')==URL(),URL('default','cloud_manage'),[]),
(T('Platform'),URL('default','platform_manage')==URL(),URL('default','platform_manage'),[]),
(T('Library Types'),URL('default','library_type_manage')==URL(),URL('default','library_type_manage'),[]),
(T('Archives'),URL('default','archives')==URL(),URL('default','archives'),[])
] ) )
def experiment_unit_manage( public , fields = basic_experiment_fields , type = None , is_active = True ):
if type<>None:
type = db( db.t_library_type.f_name == type ).select()[ 0 ][ db.t_library_type.id ]
pub = 'my'
if public:
pub = 'public'
experiment_links = [
lambda row: downloadRow( row ),
lambda row: fileRow( pub , row ),
lambda row: stateRow( row )
]
if is_active == False:
experiment_links.insert( 0 , lambda row: A('Restore', _href=URL( "default" , "bn_restore",args=[row.f_bionimbus_id,request.env.path_info])))
editable = True
arg = request.args( 0 )
if ( arg == 'view' ):
#experiment_links.append( lambda row: "http://www.opensciencedatacloud.org/keyservice/ark:/31807/bn%s" % row.f_bionimbus_id )
if db.t_experiment_unit[ request.args[ 2 ] ].f_spreadsheet <> None:
experiment_links.append( lambda row: A('Spreadsheet Download' , _href=URL("default","spreadsheet_download", args=[row.f_spreadsheet])))
if ( arg == 'edit' ):
if is_user_admin( db , auth ):
editable = True
if is_active == True:
experiment_links.insert( 0 , lambda row: A('Archive', _href=URL( "default" , "bn_archive",args=[row.f_bionimbus_id])))
else:
id = int( request.args( 2 ) )
rows = db( ( db.t_user_project.f_user_id == auth.user_id ) &
( db.t_user_project.f_admin == 'T') &
( db.t_experiment_unit.id == id ) ).select( db.t_experiment_unit.id , left = experiment_project_join(db) )
#response.flash = db._lastsql
if len(rows)<1:
response.flash = "you can't edit that experiment"
editable = False
else:
editable = True
if public == True:
q = db.t_experiment_unit.f_is_public == 't'
else:
if is_user_admin( db , auth ):
q = ( db.t_experiment_unit.id <> -1 )
else:
q = ( db.t_experiment_unit.f_project == db.t_user_project.f_project_id ) & ( db.t_user_project.f_user_id == auth.user_id )
if type <> None:
q = q & ( db.t_experiment_unit.f_library_type == type )
q = q & ( db.t_experiment_unit.is_active == is_active )
#db( q ).select()
#print db._lastsql
form = SQLFORM.grid( q ,
fields = fields ,
links = experiment_links ,
editable = editable ,
onupdate = auth.archive ,
deletable = False ,
create = False ,
maxtextlength = 150,
paginate = 100 ,
headers = { 0 : 'poopy' } ,
selectable = lambda ids: add_bn_id(ids) ,
orderby=~db.t_experiment_unit.f_sample_state_changed
)
#need this try-catch in case the table is empty, and therefore has no submit button
try:
form.element('.web2py_table input[type=submit]')['_value'] = T('Add To Dropbox')
except:
pass
return locals()
def experiment_unit_manage(public,
fields=basic_experiment_fields,
type=None,
is_active=True):
if type <> None:
type = db(
db.t_library_type.f_name == type).select()[0][db.t_library_type.id]
pub = 'my'
if public:
pub = 'public'
experiment_links = [
lambda row: downloadRow(row), lambda row: fileRow(pub, row),
lambda row: stateRow(row)
]
if is_active == False:
experiment_links.insert(
0, lambda row: A(
'Restore',
_href=URL("default",
"bn_restore",
args=[row.f_bionimbus_id, request.env.path_info])))
editable = True
arg = request.args(0)
if (arg == 'view'):
#experiment_links.append( lambda row: "http://www.opensciencedatacloud.org/keyservice/ark:/31807/bn%s" % row.f_bionimbus_id )
if db.t_experiment_unit[request.args[2]].f_spreadsheet <> None:
experiment_links.append(
lambda row: A('Spreadsheet Download',
_href=URL("default",
"spreadsheet_download",
args=[row.f_spreadsheet])))
if (arg == 'edit'):
if is_user_admin(db, auth):
editable = True
if is_active == True:
experiment_links.insert(
0, lambda row: A('Archive',
_href=URL("default",
"bn_archive",
args=[row.f_bionimbus_id])))
else:
id = int(request.args(2))
rows = db((db.t_user_project.f_user_id == auth.user_id)
& (db.t_user_project.f_admin == 'T')
& (db.t_experiment_unit.id == id)).select(
db.t_experiment_unit.id,
left=experiment_project_join(db))
#response.flash = db._lastsql
if len(rows) < 1:
response.flash = "you can't edit that experiment"
editable = False
else:
editable = True
if public == True:
q = db.t_experiment_unit.f_is_public == 't'
else:
if is_user_admin(db, auth):
q = (db.t_experiment_unit.id <> -1)
else:
q = (db.t_experiment_unit.f_project
== db.t_user_project.f_project_id) & (
db.t_user_project.f_user_id == auth.user_id)
if type <> None:
q = q & (db.t_experiment_unit.f_library_type == type)
q = q & (db.t_experiment_unit.is_active == is_active)
#db( q ).select()
#print db._lastsql
form = SQLFORM.grid(q,
fields=fields,
links=experiment_links,
editable=editable,
onupdate=auth.archive,
deletable=False,
create=False,
maxtextlength=150,
paginate=100,
headers={0: 'poopy'},
selectable=lambda ids: add_bn_id(ids),
orderby=~db.t_experiment_unit.f_sample_state_changed)
#need this try-catch in case the table is empty, and therefore has no submit button
try:
form.element('.web2py_table input[type=submit]')['_value'] = T(
'Add To Dropbox')
except:
pass
return locals()